ArticleDatabase : the journal of biological databases and curation2016
2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein-protein interactions.
Article in Database : the journal of biological databases and curation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 80 citations in OpenAlex.
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- Instance and Feature Selection: Algorithmic Identification of Unique Kinase Protein Interactions from the Protein Data Bank (PDB) and Their Features.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Evaluating ligand docking methods for drugging protein-protein interfaces: insights from AlphaFold2 and molecular dynamics refinement.Journal of cheminformatics · 2025Article
- Target Mapping in Cancer: Ligandable Protein Pockets on 3D OncoPPI Networks.Pharmaceuticals (Basel, Switzerland) · 2025Article
- DiPPI: A Curated Data Set for Drug-like Molecules in Protein-Protein Interfaces.Journal of chemical information and modeling · 2024Article
- Generating Potential Protein-Protein Interaction Inhibitor Molecules Based on Physicochemical Properties.Molecules (Basel, Switzerland) · 2023Article
- Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches.Frontiers in molecular biosciences · 2023Article
- Implications of the Essential Role of Small Molecule Ligand Binding Pockets in Protein-Protein Interactions.The journal of physical chemistry. B · 2022Article
- Structural landscapes of PPI interfaces.Briefings in bioinformatics · 2022Review
- DLiP-PPI library: An integrated chemical database of small-to-medium-sized molecules targeting protein-protein interactions.Frontiers in chemistry · 2022Article
- Quantitative Estimate Index for Early-Stage Screening of Compounds Targeting Protein-Protein Interactions.International journal of molecular sciences · 2021Article
- Exploring the chemical space of protein-protein interaction inhibitors through machine learning.Scientific reports · 2021Article
- Structural Design and Analysis of the RHOA-ARHGEF1 Binding Mode: Challenges and Applications for Protein-Protein Interface Prediction.Frontiers in molecular biosciences · 2021Article
- Literature mining for context-specific molecular relations using multimodal representations (COMMODAR).BMC bioinformatics · 2020Review
- Targeting the cryptic sites: NMR-based strategy to improve protein druggability by controlling the conformational equilibrium.Science advances · 2020Article
- Fr-PPIChem: An Academic Compound Library Dedicated to Protein-Protein Interactions.ACS chemical biology · 2020Article
- The design and development of covalent protein-protein interaction inhibitors for cancer treatment.Journal of hematology & oncology · 2020Review
- Biophysical Techniques for Target Validation and Drug Discovery in Transcription-Targeted Therapy.International journal of molecular sciences · 2020Review
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
2P2Idb is a hand-curated structural database dedicated to protein-protein interactions with known small molecule orthosteric modulators. It compiles the structural information related to orthosteric inhibitors and their target [i.e. related 3D structures available in the RCSB Protein Data Bank (PDB)] and provides links to other useful databases. 2P2Idb includes all interactions for which both the protein-protein and protein-inhibitor complexes have been structurally characterized. Since its first release in 2010, the database has grown constantly and the current version contains 27 protein-protein complexes and 274 protein-inhibitor complexes corresponding to 242 unique small molecule inhibitors which represent almost a 5-fold increase compared to the previous version. A number of new data have been added, including new protein-protein complexes, binding affinities, molecular descriptors, precalculated interface parameters and links to other webservers. A new query tool has been implemented to search for inhibitors within the database using standard molecular descriptors. A novel version of the 2P2I-inspector tool has been implemented to calculate a series of physical and chemical parameters of the protein interfaces. Several geometrical parameters including planarity, eccentricity and circularity have been added as well as customizable distance cutoffs. This tool has also been extended to protein-ligand interfaces. The 2P2I database thus represents a wealth of structural source of information for scientists interested in the properties of protein-protein interactions and the design of protein-protein interaction modulators. Database URL: http://2p2idb.cnrs-mrs.fr.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.